Hi all,
I'm trying to use cpptraj to compute the RMSD between my trajectory and a crystal structure. The script works fine, but the RMSD values seems incorrect. My reference is this clean_update.pdb. it has the same residues as the protein in my trajectory. The first rms command produced RMSD at around 6 Ang for all the snapshots, but when I look at the final structure overlay produced by my "trajout" command, the two structures do not look like they are 6 Ang apart. Also after the alignment from the first rms command, I wrote down the distance between two CA atoms from resid 100, the output rmsd_test2.plo show that they are 4 Ang apart, though in the superposed pdb files they are only 0.5 Ang away. Here's how my cpptraj script look like:
trajin step4_1.nc 1 500 1
parm clean_update.pdb
reference clean_update.pdb parm clean_update.pdb
autoimage :1-170
rms reference :3-165.CA :3-165.CA out rmsd_test.plo
rms reference :100.CA :100.CA nofit out rmsd_test2.plo
trajout testrmsd.pdb onlyframes 500
run
quit
Could anybody give me some insights on why this is?
Thank you very much in advance.
Thanks,
Huan
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Received on Fri Feb 09 2018 - 12:00:02 PST
